suppressPackageStartupMessages({
library(tidyverse)
library(plotly)
library(treeio)
library(ggtree)
library(ggtreeExtra)
library(svglite)
})
BGC table for Myxococcota
## # A tibble: 7,616 × 9
## bgc_id GCF genome_id contig start end product contig_edge class
## <chr> <chr> <chr> <chr> <dbl> <dbl> <chr> <lgl> <chr>
## 1 BBEO01000017.1.… 0 GCA_0013… BBEO0… 0 5749 NRPS TRUE NRPS
## 2 BBEO01000114.1.… 1 GCA_0013… BBEO0… 0 3507 RiPP-l… TRUE RiPPs
## 3 BBEO01000191.1.… 2 GCA_0013… BBEO0… 0 3019 T1PKS TRUE PKSI
## 4 BBEO01000385.1.… 3 GCA_0013… BBEO0… 0 2351 NRPS TRUE NRPS
## 5 BBEO01000617.1.… 4 GCA_0013… BBEO0… 0 1970 NRPS-l… TRUE NRPS
## 6 BBEO01000880.1.… 4782… GCA_0013… BBEO0… 0 1694 resorc… TRUE Othe…
## 7 BBEO01000892.1.… 6;67… GCA_0013… BBEO0… 0 1685 proteu… TRUE RiPPs
## 8 BJHF01000010.1.… 1918 GCA_0141… BJHF0… 77871 88714 RiPP-l… FALSE RiPPs
## 9 BJHF01000022.1.… 1919 GCA_0141… BJHF0… 21748 66476 arylpo… FALSE Othe…
## 10 BJHF01000033.1.… 1920 GCA_0141… BJHF0… 19254 59021 hglE-KS TRUE PKSo…
## # … with 7,606 more rows
Genome table for Myxococcota
## # A tibble: 572 × 11
## genome_id total_bgcs bgcs_on_contig_edge gtdb_taxonomy assembly_level
## <chr> <dbl> <dbl> <chr> <chr>
## 1 GCA_016704525.1 8 1 d__Bacteria;p_… Contig/Scaffo…
## 2 GCA_016704445.1 12 3 d__Bacteria;p_… Contig/Scaffo…
## 3 GCA_016704335.1 16 2 d__Bacteria;p_… Contig/Scaffo…
## 4 GCA_016704065.1 11 5 d__Bacteria;p_… Contig/Scaffo…
## 5 GCA_016703535.1 13 0 d__Bacteria;p_… Contig/Scaffo…
## 6 GCA_016703425.1 18 0 d__Bacteria;p_… Contig/Scaffo…
## 7 GCA_016702865.1 12 5 d__Bacteria;p_… Contig/Scaffo…
## 8 GCA_016702545.1 11 1 d__Bacteria;p_… Contig/Scaffo…
## 9 GCA_016709225.1 20 0 d__Bacteria;p_… Contig/Scaffo…
## 10 GCA_016708565.1 12 2 d__Bacteria;p_… Contig/Scaffo…
## # … with 562 more rows, and 6 more variables: checkm_completeness <dbl>,
## # checkm_contamination <dbl>, genome_size <dbl>, ncbi_bioproject <chr>,
## # mimag_quality <chr>, source <chr>
Customize BiG-SCAPE classes and color palette
bigscape_classes <- c("Terpene",
"RiPPs",
"NRPS",
"PKS-NRP_Hybrids",
"PKSI",
"PKSother",
"Saccharides",
"Others")
my_classes <- c("Terpene",
"RiPP",
"NRPS",
"NRPS-PKS",
"PKS",
"PKS",
"Other",
"Other")
my_colors <- c("#ff8800",
"#20c200",
"#ff0000",
"#dd00ff",
"#0d00ff",
"#757575")
QC Boxplots for the phylum Nitrospirota
What family should we focus on? Polyangiaceae is well represented by our MAGs and the references.
Overview of the phylum Myxococcota. Add number of MAGs per clade
Absence / Presence matrix for f__Polyangiaceae